So at the ending of chapter 1 i had some questions about siding with jadus. Now I like the vision that jadus has of the empire, and i agree with him wanting to cut out the rot so to say. However, I also know that openly defying the dark council and the emperor is foolish. So, my question is this: if i side with Jadus, is this public knowledge? Or a secret unless i offer up the information?

It seems like a complete joke if I side with jadus openly, the dark council would snuff me out someway, and i'd be despised by all.

Imperial Intelligence knows because of Watcher 2, but I doubt everyone there knows just a small select named personnel. The Sith/Dark Council knows and that is explained later in Chapter 2 what they do about it.

The public story of Darth Jadus' return will be different depending on if you help him or not. He will be considered either a hero or a traitor. The Dark Council will be aware of what happened. However, if you side with him, Darth Jadus becomes the new de facto leader of the Dark Council, and therefore you will have "legitimate" authority. Darth Jadus is also correct when he says that the Emperor is distracted. Since Darth Jadus is "only" trying to make a power play against the Dark Council, and not trying to supplant or co-opt the Emperor's authority, he doesn't care.